Ensembl Plants Project Leader

Grading
7 (monthly salary starting at £3,250 after tax). For more information about pay and benefits click here

Reference number
EBI_01137

Job description
We are seeking project leader to join the Non-vertebrate Genomics Team at the European Bioinformatics Institute (EMBL-EBI), located on the Wellcome Trust Genome Campus. The appointee will be responsible for the development of the Ensembl Plants resource.

Ensembl Plants is a leading global database for plant genomes. Developed using the Ensembl software framework, Ensembl Plants provides access to genome sequence, gene annotation, and analysis tools to large numbers of researchers working in many different species. We are part of the United Kingdom’s Designing Future Wheat program, which brings together eight organisations aiming to assist in the development of improved wheat varieties; European and trans-Atlantic collaborations (in the ELIXIR and Gramene projects); and are working with the community to develop new data standards and tools to assist in the collection and dissemination of data. We are looking for a new staff member to take responsibility for this project.

The project leader’s working life will be varied, and will involve supervising staff; interacting with our collaborators, with data generators, and with the user community; contributing to data releases and development of the Ensembl code base; and developing operating procedures, code specifications, and priorities for future work. They will need to work closely with other staff contributing to the Ensembl services, and will be expected to contribute to the preparation of reports due to funding agencies, and to applications for additional funding. The post would suit an experienced bioinformatician, ideally one with established connections to the European plant research community, with an interest in, and ideas for, developing services that facilitate genomic-driven research. If you join us, you will find a supportive environment, outstanding local know-how, and a robust infrastructure and toolset to form the basis for the basis for the services whose development you will oversee.

At EMBL-EBI, we help scientists realise the potential of ‘big data’ in biology by enabling them to exploit complex information to make discoveries that benefit mankind. Working for EMBL-EBI gives you an opportunity to apply your skills and energy for the greater good. As part of the European Molecular Biology Laboratory (EMBL), we are a non-profit, intergovernmental organisation funded by 23 member states and two associate member states and proud to be an equal-opportunity employer. We are located on the Wellcome Genome Campus near Cambridge in the UK, and our 600 staff are engineers, technicians, scientists and other professionals from all over the world.

Qualifications and experience
Applicants should have at least five years -experience working in bioinformatics, with at least two years working in a service capacity. Research experience, and experience of working with on plants, are both desirable but not essential. The successful candidate will be familiar with many of the types of data we handle in Ensembl Plants (including but not limited to short read sequencing data, variant call data, and multiple sequencing alignments) and aware of the common approaches and pitfalls when dealing with them. They will be familiar with Ensembl Plants and ideally have a working knowledge of other leading biomolecular archives and resources. They will possess excellent communication and interpersonal skills.

Computational expertise is also necessary: the applicant is expected to be familiar with Linux, relational database management systems, and at least one programming language. Experience of code repositories, compute farms and queuing systems, containers, and other tools for software development and deployment will be considered favourably.

Benefits
You will hold a degree in computer science or bioinformatics, or a degree in biological sciences and a post-graduate qualification in computer science or bioinformatics. Experience working in genomics, insect biology, epidemiology, or bioinformatics is highly desirable, but not essential.

A minimum of two years professional programming experience or research experience with next generation sequencing data is needed. Experience of working in a dynamic, team-based environment and contributing to a shared code-base is desirable.

You must be highly self-motivated, and be able to work independently and manage your time effectively. You must also be open to working in a production team (willing to conform and contribute to standard working practices); and are expected to have good communication skills, written and verbal, both to facilitate effective communications with other team members and to communicate with external collaborators and users.

The successful candidate will have good knowledge of Perl, though experience in other scripting languages (e.g. Python, JavaScript) or compiled languages (e.g. Java) will also be taken into consideration. Knowledge of relational database management systems (e.g. MySQL), writing SQL statements and designing database schemas is essential. Experience of using Ensembl, indexing systems (e.g.Solr), handling large data sets, workflow management systems for distributed computing (e.g. LSF, SGE), NoSQL database technologies, and of the use of biological ontologies for data annotation, are all desirable.

How to apply
To apply please submit a covering letter and CV, with two referees, through our online system.